# Copyright 2012 Tobias Marschall
# 
# This file is part of CLEVER.
# 
# CLEVER is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# CLEVER is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with CLEVER.  If not, see <http://www.gnu.org/licenses/>.

add_executable ( bam-to-alignment-priors
	bam-to-alignment-priors.cpp
	InsertLengthDistribution.cpp
	GroupWiseBamReader.cpp
)

add_executable (clever 
	clever.cpp
	AlignmentPair.cpp
	PackedAlignmentPair.cpp
	CliqueFinder.cpp
	Clique.cpp
	EdgeCalculator.cpp
	CliqueWriter.cpp
	CoverageMonitor.cpp
	EdgeWriter.cpp
	CoverageWriter.cpp
	Variation.cpp
	VariationCaller.cpp
)

add_executable (generate-smart-input
	generate-smart-input.cpp
	AlignmentPair.cpp
	ReadAssignmentFileReader.cpp
	Variation.cpp
	VariationIndex.cpp
	VariationListParser.cpp
	LengthAwareVariationIndex.cpp
)

add_executable (insert-length-histogram
	insert-length-histogram.cpp
)

add_executable ( add-score-tags-to-bam
	add-score-tags-to-bam.cpp
	NamedDnaSequence.cpp
	ASTagCalculator.cpp
	GroupWiseBamReader.cpp
)

target_link_libraries(bam-to-alignment-priors ${Boost_LIBRARIES} BamTools)
target_link_libraries(clever ${Boost_LIBRARIES})
target_link_libraries(generate-smart-input ${Boost_LIBRARIES})
target_link_libraries(insert-length-histogram ${Boost_LIBRARIES} BamTools)
target_link_libraries(add-score-tags-to-bam ${Boost_LIBRARIES} BamTools)
install(TARGETS bam-to-alignment-priors insert-length-histogram clever generate-smart-input add-score-tags-to-bam RUNTIME DESTINATION bin)
